[gmx-users] protein fragmented issue for minimization

Justin Lemkul jalemkul at vt.edu
Wed Dec 13 20:40:49 CET 2017

On 12/13/17 1:27 PM, MD wrote:
> How about letting gromacs think that it is one protein with two chains?

You can do that, but whether or not it makes sense is up to you. I'd say 
that in general, lazily choosing to not model in a missing segment is 
going to cause people to not believe your work. You'll get a lot of 
artificiality at the fake termini.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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